diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 23f60b3..fb9c43b 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 1.2.1
+current_version = 1.2.2
commit = True
tag = True
diff --git a/calphy/__init__.py b/calphy/__init__.py
index ab8eac0..44b9282 100644
--- a/calphy/__init__.py
+++ b/calphy/__init__.py
@@ -4,7 +4,7 @@
from calphy.alchemy import Alchemy
from calphy.routines import MeltingTemp
-__version__ = "1.2.1"
+__version__ = "1.2.2"
def addtest(a,b):
return a+b
diff --git a/calphy/alchemy.py b/calphy/alchemy.py
index da8d3f9..c4499e5 100644
--- a/calphy/alchemy.py
+++ b/calphy/alchemy.py
@@ -155,6 +155,7 @@ def run_integration(self, iteration=1):
#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
+ lmp.command("velocity all create %f %d mom yes rot yes dist gaussian"%(self.calc._temperature, np.random.randint(0, 10000)))
# Integrator & thermostat.
if self.calc._npt:
lmp.command("fix f1 all npt temp %f %f %f %s %f %f %f"%(self.calc._temperature, self.calc._temperature,
@@ -321,8 +322,8 @@ def thermodynamic_integration(self):
def mass_integration(self, flambda, ref_mass, target_masses, target_counts):
- mcorarr = integrate_mass(flambda, ref_mass, target_masses, target_counts,
+ mcorarr, mcorsum = integrate_mass(flambda, ref_mass, target_masses, target_counts,
self.calc._temperature, self.natoms)
- return mcorarr
+ return mcorarr, mcorsum
diff --git a/calphy/input.py b/calphy/input.py
index 749fe3b..51164e8 100644
--- a/calphy/input.py
+++ b/calphy/input.py
@@ -30,6 +30,18 @@
import shutil
import numpy as np
+def read_report(folder):
+ """
+ Read the finished calculation report
+ """
+ repfile = os.path.join(folder, "report.yaml")
+ if not os.path.exists(repfile):
+ raise FileNotFoundError(f"file {repfile} not found")
+
+ with open(repfile, 'r') as fin:
+ data = yaml.safe_load(fin)
+ return data
+
class InputTemplate:
def __init__(self):
pass
@@ -93,7 +105,6 @@ def merge_dicts(self, dicts):
merged_dict[key] = val
return merged_dict
-
class CompositionScaling(InputTemplate):
def __init__(self):
self._input_chemical_composition = None
@@ -157,6 +168,7 @@ def __init__(self):
self._n_print_steps = 0
self._n_iterations = 1
self._equilibration_control = None
+ self._folder_prefix = None
#add second level options; for example spring constants
self._spring_constants = None
@@ -549,6 +561,14 @@ def spring_constants(self, val):
val = self.check_and_convert_to_list(val, check_none=True)
self._spring_constants = val
+ @property
+ def folder_prefix(self):
+ return self._folder_prefix
+
+ @folder_prefix.setter
+ def folder_prefix(self, val):
+ self._folder_prefix = val
+
def fix_paths(self, potlist):
"""
Fix paths for potential files to complete ones
@@ -594,7 +614,11 @@ def create_identifier(self):
l = self.lattice
l = l.split('/')
l = l[-1]
- identistring = "-".join([prefix, l, str(ts), str(ps)])
+
+ if self.folder_prefix is None:
+ identistring = "-".join([prefix, l, str(ts), str(ps)])
+ else:
+ identistring = "-".join([self.folder_prefix, prefix, l, str(ts), str(ps)])
return identistring
def create_folders(self, prefix=None):
@@ -688,7 +712,8 @@ def read_inputfile(file):
if mode == "melting_temperature":
calc = Calculation.generate(indata)
calc.add_from_dict(ci, keys=["mode", "pair_style", "pair_coeff", "repeat", "n_equilibration_steps",
- "n_switching_steps", "n_print_steps", "n_iterations", "spring_constants", "equilibration_control"])
+ "n_switching_steps", "n_print_steps", "n_iterations", "spring_constants", "equilibration_control",
+ "folder_prefix"])
calc.pressure = Calculation.convert_to_list(ci["pressure"], check_none=True) if "pressure" in ci.keys() else 0
calc.temperature = Calculation.convert_to_list(ci["temperature"]) if "temperature" in ci.keys() else None
calc.lattice = Calculation.convert_to_list(ci["lattice"]) if "lattice" in ci.keys() else None
@@ -724,7 +749,7 @@ def read_inputfile(file):
calc = Calculation.generate(indata)
calc.add_from_dict(ci, keys=["mode", "pair_style", "pair_coeff", "repeat", "n_equilibration_steps",
"n_switching_steps", "n_print_steps", "n_iterations", "potential_file", "spring_constants",
- "melting_cycle", "equilibration_control"])
+ "melting_cycle", "equilibration_control", "folder_prefix"])
calc.lattice = combo[0]["lattice"]
calc.lattice_constant = combo[0]["lattice_constant"]
calc.reference_phase = combo[0]["reference_phase"]
diff --git a/calphy/integrators.py b/calphy/integrators.py
index db729f8..d0d52e9 100644
--- a/calphy/integrators.py
+++ b/calphy/integrators.py
@@ -360,15 +360,15 @@ def find_w(mainfolder, nelements=1, concentration=[1,], nsims=5, full=False, use
if composition_integration:
wsmean = np.mean(ws, axis=0)
qsmean = np.mean(qs, axis=0)
- qsstd = np.mean(qs, axis=0)
- return wsmean, qsmean, qsstd, flambda
+ wsstd = np.std(ws, axis=0)
+ return wsmean, qsmean, wsstd, flambda
wsmean = np.mean(ws)
qsmean = np.mean(qs)
- qsstd = np.mean(qs)
+ wsstd = np.std(ws)
if full:
- return wsmean, qsmean, qsstd
+ return wsmean, qsmean, wsstd
else:
return wsmean
@@ -671,7 +671,10 @@ def integrate_mass(flambda, ref_mass, target_masses, target_counts,
temperature, natoms):
mcorarr = np.zeros(len(flambda))
+ mcorsum = 0
+
for i in range(len(target_masses)):
mcorarr += 1.5*kb*temperature*(flambda*(target_counts[i]/natoms)*np.log(ref_mass/target_masses[i]))
-
- return mcorarr
\ No newline at end of file
+ mcorsum += 1.5*kb*temperature*(1.0*(target_counts[i]/natoms)*np.log(ref_mass/target_masses[i]))
+
+ return mcorarr, mcorsum
\ No newline at end of file
diff --git a/calphy/phase.py b/calphy/phase.py
index 9e58e73..3c23f14 100644
--- a/calphy/phase.py
+++ b/calphy/phase.py
@@ -178,6 +178,15 @@ def __repr__(self):
data = self.calc.__repr__()
return data
+ def _from_dict(self, org_dict, indict):
+ for key, val in indict.items():
+ if isinstance(val, dict):
+ if key not in org_dict.keys():
+ org_dict[key] = {}
+ self._from_dict(org_dict[key], val)
+ else:
+ org_dict[key] = val
+
def prepare_lattice(self):
"""
Prepare the lattice for the simulation
@@ -564,13 +573,14 @@ def process_traj(self, filename, outfilename):
os.remove(file)
- def submit_report(self):
+ def submit_report(self, extra_dict=None):
"""
Submit final report containing results
Parameters
----------
- None
+ extra_dict: dict
+ extra information to be written out
Returns
-------
@@ -602,6 +612,10 @@ def submit_report(self):
report["results"]["reference_system"] = float(self.fref)
report["results"]["work"] = float(self.w)
report["results"]["pv"] = float(self.pv)
+
+ if extra_dict is not None:
+ self._from_dict(report, extra_dict)
+
self.report = report
reportfile = os.path.join(self.simfolder, "report.yaml")
diff --git a/calphy/routines.py b/calphy/routines.py
index 8f7d37b..c867a27 100644
--- a/calphy/routines.py
+++ b/calphy/routines.py
@@ -514,9 +514,12 @@ def routine_composition_scaling(job):
flambda_arr, w_arr, q_arr, qerr_arr = job.thermodynamic_integration()
#read the file
- mcorrarr = job.mass_integration(flambda_arr, ref_mass, target_masses, target_counts)
+ mcorrarr, mcorsum = job.mass_integration(flambda_arr, ref_mass, target_masses, target_counts)
netfe = w_arr - mcorrarr
+ job.fe = job.fe - mcorsum
+ job.submit_report(extra_dict = {"results":{"mass_correction": float(mcorsum)}})
+
outfile = os.path.join(job.simfolder, "composition_sweep.dat")
np.savetxt(outfile, np.column_stack((flambda_arr, netfe, w_arr, mcorrarr)))
return job
\ No newline at end of file
diff --git a/docs/source/documentation/inputfile.md b/docs/source/documentation/inputfile.md
index eee4b49..04c8573 100644
--- a/docs/source/documentation/inputfile.md
+++ b/docs/source/documentation/inputfile.md
@@ -12,7 +12,7 @@ The inputfile is `yaml` formatted. In this section the possible keys in the inpu
| [mode](#mode) | [lattice](#lattice) | [reference_phase](#reference_phase) | [temperature](#temperature) | [pressure](#pressure) |
| [temperature_high](#temperature_high) | [lattice_constant](#lattice_constant) | [repeat](#repeat) | [n_iterations](#n_iterations) | [n_switching_steps](#n_switching_steps) |
| [n_equilibration_steps](#n_equilibration_steps) | [pair_style](#pair_style) | [pair_coeff](#pair_coeff) | [n_print_steps](#n_print_steps) | [potential_file](#potential_file) |
-| [spring_constants](#spring_constants) | [equilibration_control](#equilibration_control) | [melting_cycle](#melting_cycle) | | |
+| [spring_constants](#spring_constants) | [equilibration_control](#equilibration_control) | [melting_cycle](#melting_cycle) | [folder_prefix](#folder_prefix) | |
| `md` block | | | | |
| :-: | :-: | :-: | :-: | :-: |
@@ -32,6 +32,10 @@ The inputfile is `yaml` formatted. In this section the possible keys in the inpu
| :-: | :-: | :-: | :-: | :-: |
| [step](#step) | [attempts](#attempts) |
+| `composition_scaling` block | | | | |
+| :-: | :-: | :-: | :-: | :-: |
+| [input_chemical_composition](#input_chemical_composition) | [output_chemical_composition](#output_chemical_composition) |
+
| `nose_hoover` block | | | | |
| :-: | :-: | :-: | :-: | :-: |
| [thermostat_damping](#nose_hoover_thermostat_damping) | [barostat_damping](#nose_hoover_barostat_damping) |
@@ -384,6 +388,20 @@ melting_cycle: False
If True, a melting cycle is carried out to melt the given input structure. Only used if the `reference_phase` is `"liquid"`.
+
+---
+
+#### `folder_prefix`
+
+_type_: string
+_default_: None
+_example_:
+```
+folder_prefix: set1
+```
+
+Prefix string to be added to folder names for calculation. Folders for calculations in calphy are named as `mode-lattice-temperature-pressure`. Therefore, if more than one calculation is run with the same parameters, they will be overwritten. To prevent this, `folder_prefix` can be used. If `folder_prefix` is provided, the folders will be named as `folder_prefix-mode-lattice-temperature-pressure`.
+
---
---
@@ -731,6 +749,51 @@ The number of maximum attempts to try find the melting temperature in a automate
---
---
+## `composition_scaling` block
+
+This block contains keywords that are used only for the mode `composition_scaling`.
+
+```
+composition_scaling:
+ input_chemical_composition:
+ - Cu: 512
+ - Zr: 512
+ output_chemical_composition:
+ - Cu: 513
+ - Zr: 511
+```
+
+---
+
+#### `input_chemical_composition`
+
+_type_: list
+_example_:
+```
+input_chemical_composition:
+ - Cu: 512
+ - Zr: 512
+```
+
+The input chemical composition in number of atoms. It should be identical to the input structure provided.
+
+---
+
+#### `output_chemical_composition`
+
+_type_: list
+_example_:
+```
+output_chemical_composition:
+ - Cu: 513
+ - Zr: 511
+```
+
+The output chemical composition in number of atoms. The total number of atoms should be equal to the input provided.
+
+---
+---
+
## `nose_hoover` block
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
index f57740a..e2c3ab1 100644
--- a/docs/source/examples.rst
+++ b/docs/source/examples.rst
@@ -12,3 +12,4 @@ Examples
examples/example_07/analysis
examples/example_08/analysis
examples/example_09/analysis
+ examples/example_10/analysis
diff --git a/environment-nolammps.yml b/environment-nolammps.yml
index cc05cc7..5a27797 100644
--- a/environment-nolammps.yml
+++ b/environment-nolammps.yml
@@ -15,3 +15,4 @@ dependencies:
- pyscal
- matplotlib
- tqdm
+ - uncertainties
diff --git a/environment.yml b/environment.yml
index be38c5e..8de1b34 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,3 +13,4 @@ dependencies:
- pyscal
- matplotlib
- tqdm
+ - uncertainties
diff --git a/examples/example_10/ZrCu_substitution.dump b/examples/example_10/ZrCu_substitution.dump
new file mode 100644
index 0000000..3833dba
--- /dev/null
+++ b/examples/example_10/ZrCu_substitution.dump
@@ -0,0 +1,1033 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+1024
+ITEM: BOX BOUNDS
+0.000000 26.160000
+0.000000 26.160000
+0.000000 26.160000
+ITEM: ATOMS id type x y z
+1 1 0.000000 0.000000 0.000000
+2 2 1.635000 1.635000 1.635000
+3 1 0.000000 0.000000 3.270000
+4 2 1.635000 1.635000 4.905000
+5 1 0.000000 0.000000 6.540000
+6 2 1.635000 1.635000 8.175000
+7 1 0.000000 0.000000 9.810000
+8 2 1.635000 1.635000 11.445000
+9 1 0.000000 0.000000 13.080000
+10 2 1.635000 1.635000 14.715000
+11 2 0.000000 0.000000 16.350000
+12 2 1.635000 1.635000 17.985000
+13 1 0.000000 0.000000 19.620000
+14 2 1.635000 1.635000 21.255000
+15 1 0.000000 0.000000 22.890000
+16 2 1.635000 1.635000 24.525000
+17 1 0.000000 3.270000 0.000000
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+20 2 1.635000 4.905000 4.905000
+21 1 0.000000 3.270000 6.540000
+22 2 1.635000 4.905000 8.175000
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+24 2 1.635000 4.905000 11.445000
+25 1 0.000000 3.270000 13.080000
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diff --git a/examples/example_10/analysis.ipynb b/examples/example_10/analysis.ipynb
index cd004e1..435e73d 100644
--- a/examples/example_10/analysis.ipynb
+++ b/examples/example_10/analysis.ipynb
@@ -20,7 +20,114 @@
"\n",
"[M.I. Mendelev , M.J. Kramer , R.T. Ott , D.J. Sordelet , D. Yagodin & P. Popel (2009) Development of suitable interatomic potentials for simulation of liquid and amorphous Cu–Zr alloys, Philosophical Magazine, 89:11, 967-987](http://dx.doi.org/10.1080/14786430902832773)\n",
"\n",
- "We specify the mode as `composition_scaling` in the input file. The input file has a new section:\n",
+ "In the first part of the example, a simple free energy difference that happens when a substitutional atom is introduced is calculated in two ways. In the second part, we directly calculate the free energy as the composition varies in the given system."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "839c412e-5448-49c3-9ac2-6ac36ef6ae05",
+ "metadata": {},
+ "source": [
+ "## Free energy change with substitutional atom"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0072d247-40eb-467b-9b26-4efe2be4e66b",
+ "metadata": {},
+ "source": [
+ "In the file [`ZrCu.dump`](ZrCu.dump), CuZr in B2 structure is provided. The file [`ZrCu_substitution.dump`](ZrCu_substitution.dump) contains the same structure, but a single atom of Zr is replaced with Cu. If the free energy of both structures are calculated, the difference between the two provides the free energy change when a substitutional Cu atom is introduced.\n",
+ "\n",
+ "The input files for the direct calculations are [`input-direct-1.yaml`](input-direct-1.yaml) and [`input-direct-2.yaml`](input-direct-2.yaml). The calculations can be run by `calphy -i inputfilename`. Once the calculations are over, we can read in the results and analyse them."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "48d15362-3fdf-43bd-84ca-851c30b68da5",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import numpy as np\n",
+ "import matplotlib.pyplot as plt\n",
+ "from calphy.input import read_report\n",
+ "from uncertainties import ufloat"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "ecb50326-8214-41ef-8568-7e8ecf1e37a3",
+ "metadata": {},
+ "source": [
+ "We import the `read_report` method as shown above. This allows for easy reading of calphy output files. The data from the pure structure is read into `fe_ref_direct` and the data with the substitutional atom is in `fe_sub_direct`. We also import the [`uncertainties`](https://pythonhosted.org/uncertainties/) package, which will allow us to work with error bars."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "b10bc8f8-1b90-4767-a898-ad85bb2d3eb8",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fe_ref_direct = read_report(\"fe-ZrCu.dump-800-0\")\n",
+ "fe_sub_direct = read_report(\"fe-ZrCu_substitution.dump-800-0\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "afd15c4d-5f97-405d-bd02-61e4df3c5d6f",
+ "metadata": {},
+ "source": [
+ "Now calculate the difference in free energy between the two structures. We create `ufloat` objects to do operations including error bars."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "9255fe4d-a45d-46cb-b462-92dfe8586974",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fe_ref = ufloat(fe_ref_direct[\"results\"][\"free_energy\"], fe_ref_direct[\"results\"][\"error\"])\n",
+ "fe_sub = ufloat(fe_sub_direct[\"results\"][\"free_energy\"], fe_sub_direct[\"results\"][\"error\"])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "5dfe77b6-23bb-4456-acec-fb3fd68b79e4",
+ "metadata": {},
+ "source": [
+ "Now the difference"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "476a6026-b44c-4ce8-b055-97bb07a2c465",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.0036244140356958+/-0.0005247047613173691"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "fe_sub - fe_ref"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "85b3d803-3d31-4039-9ec8-842b6125d05e",
+ "metadata": {},
+ "source": [
+ "Another way to do the same calculation is through the `composition_scaling` mode in calphy. The input is given in the file [`input-substitution.yaml`](input-substitution.yaml). The mode is `composition_scaling`. Further more, there is a new block in the input file:\n",
+ "\n",
"\n",
"```\n",
"composition_scaling:\n",
@@ -28,11 +135,11 @@
" - Cu: 512\n",
" - Zr: 512\n",
" output_chemical_composition:\n",
- " - Cu: 532\n",
- " - Zr: 492\n",
+ " - Cu: 513\n",
+ " - Zr: 511\n",
"```\n",
"\n",
- "which provides the details for composition change. The `input_chemical_composition` shows equal number of Cu and Zr atoms as expected in the B2 structure. The `output_chemical_composition` has 532 Cu and 492 Zr atoms, which amounts to 48 at. % Zr. The composition integration therefore will span 48-50% of Zr.\n",
+ "which provides the details for composition change. The `input_chemical_composition` shows equal number of Cu and Zr atoms as expected in the B2 structure. The `output_chemical_composition` has 513 Cu and 511 Zr atoms, which means that one Cu atom is substituted for Zr over the calculation.\n",
"\n",
"As usual, the calculation can be run by:\n",
"\n",
@@ -40,23 +147,88 @@
"calphy -i input.yaml\n",
"```\n",
"\n",
- "Once the calculation is run, there is a file `composition_scaling.dat` created in the simulation folder. We can read in this file, to get the information. There are a number of columns in the file, but we will just use the first two."
+ "Once the calculation is over, we can read in the data."
]
},
{
"cell_type": "code",
- "execution_count": 1,
- "id": "48d15362-3fdf-43bd-84ca-851c30b68da5",
+ "execution_count": 8,
+ "id": "6633d120-1d07-4ae6-91bd-27c2ea16804a",
"metadata": {},
"outputs": [],
"source": [
- "import numpy as np\n",
- "import matplotlib.pyplot as plt"
+ "fe_sub_comp = read_report(\"sub-composition_scaling-ZrCu.dump-800-0\")"
]
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 9,
+ "id": "a138085b-a32f-408a-a0e6-c71006fd3a30",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.0037993834787761636+/-1.1368085265609911e-05"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "fe_sub_comp = ufloat(fe_sub_comp[\"results\"][\"free_energy\"], fe_sub_comp[\"results\"][\"error\"])\n",
+ "fe_sub_comp"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "91e5c163-9f5e-4644-8994-e2e814cc35aa",
+ "metadata": {},
+ "source": [
+ "Both approaches we tried agree very well with each other. The second method needs only one single calculation instead of two different ones, and exhibits lower error overall. We can extend this approach to find the free energy as a function of the composition over a given range."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "3b63d367-bde8-4d61-b398-37e1612ba020",
+ "metadata": {},
+ "source": [
+ "## Free energy variation with composition"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "c7835069-e1f5-48f2-a319-d0a4235703c5",
+ "metadata": {},
+ "source": [
+ "The `composition_scaling` block in the input file looks slightly different here:\n",
+ "\n",
+ "```\n",
+ "composition_scaling:\n",
+ " input_chemical_composition:\n",
+ " - Cu: 512\n",
+ " - Zr: 512\n",
+ " output_chemical_composition:\n",
+ " - Cu: 532\n",
+ " - Zr: 492\n",
+ "```\n",
+ "\n",
+ "Once again, the `input_chemical_composition` shows equal number of Cu and Zr atoms, as expected in the B2 structure. The `output_chemical_composition` has 532 Cu and 492 Zr atoms, which amounts to 48 at. % Zr. The composition integration therefore will span 48-50% of Zr.\n",
+ "\n",
+ "As usual, the calculation can be run by:\n",
+ "\n",
+ "```\n",
+ "calphy -i input.yaml\n",
+ "```\n",
+ "\n",
+ "Once the calculation is run, there is a file `composition_scaling.dat` created in the simulation folder. We can read in this file, to get the information. There are a number of columns in the file, but we will just use the first two."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
"id": "b430d8a6-9da6-4245-b151-7c064ca41909",
"metadata": {},
"outputs": [],
@@ -75,7 +247,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 11,
"id": "c57c37f3-2563-421b-9c7c-1d0767b817fa",
"metadata": {},
"outputs": [],
@@ -95,7 +267,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 12,
"id": "3810bf00-f36e-4da7-8dee-253d12bdf0b6",
"metadata": {},
"outputs": [],
@@ -114,7 +286,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 13,
"id": "54710468-f710-4bc9-b010-f07ee59b3978",
"metadata": {},
"outputs": [],
@@ -133,7 +305,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 14,
"id": "0a890009-bc3c-4dd4-977f-4dc156b41dbc",
"metadata": {},
"outputs": [
@@ -166,14 +338,6 @@
"source": [
"As seen from the plot, we have excellent agreement. However, we can obtain the whole range from a single calculation."
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "de0b31d3-b01f-454a-9266-0b6b2ec457cc",
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
diff --git a/examples/example_10/input-direct-1.yaml b/examples/example_10/input-direct-1.yaml
new file mode 100644
index 0000000..dc75e2d
--- /dev/null
+++ b/examples/example_10/input-direct-1.yaml
@@ -0,0 +1,17 @@
+element: ['Zr', 'Cu']
+mass: [91.224, 63.546]
+calculations:
+- mode: fe
+ temperature: 800
+ pressure: [0]
+ lattice: [ZrCu.dump]
+ n_iterations: 3
+ reference_phase: solid
+ pair_style: eam/fs
+ pair_coeff: "* * ../potentials/ZrCu.eam.fs Zr Cu"
+ n_equilibration_steps: 5000
+ n_switching_steps: 5000
+
+queue:
+ scheduler: local
+ cores: 4
diff --git a/examples/example_10/input-direct-2.yaml b/examples/example_10/input-direct-2.yaml
new file mode 100644
index 0000000..ba23aca
--- /dev/null
+++ b/examples/example_10/input-direct-2.yaml
@@ -0,0 +1,17 @@
+element: ['Zr', 'Cu']
+mass: [91.224, 63.546]
+calculations:
+- mode: fe
+ temperature: 800
+ pressure: [0]
+ lattice: [ZrCu_substitution.dump]
+ n_iterations: 3
+ reference_phase: solid
+ pair_style: eam/fs
+ pair_coeff: "* * ../potentials/ZrCu.eam.fs Zr Cu"
+ n_equilibration_steps: 5000
+ n_switching_steps: 5000
+
+queue:
+ scheduler: local
+ cores: 4
diff --git a/examples/example_10/input-substitution.yaml b/examples/example_10/input-substitution.yaml
new file mode 100644
index 0000000..af59fbd
--- /dev/null
+++ b/examples/example_10/input-substitution.yaml
@@ -0,0 +1,26 @@
+element: ['Zr', 'Cu']
+mass: [91.224, 63.546]
+calculations:
+- mode: composition_scaling
+ temperature: 800
+ pressure: [0]
+ lattice: [ZrCu.dump]
+ n_iterations: 3
+ reference_phase: solid
+ pair_style: eam/fs
+ pair_coeff: "* * ../potentials/ZrCu.eam.fs Zr Cu"
+ n_equilibration_steps: 5000
+ n_switching_steps: 5000
+ folder_prefix: sub
+
+composition_scaling:
+ input_chemical_composition:
+ - Cu: 512
+ - Zr: 512
+ output_chemical_composition:
+ - Cu: 513
+ - Zr: 511
+
+queue:
+ scheduler: local
+ cores: 4
diff --git a/setup.py b/setup.py
index 7b2da5a..b8362ba 100644
--- a/setup.py
+++ b/setup.py
@@ -60,7 +60,7 @@
test_suite='tests',
tests_require=test_requirements,
url='https://github.com/ICAMS/calphy',
- version='1.2.1',
+ version='1.2.2',
zip_safe=False,
entry_points={
'console_scripts': [